Owen proved ineffectual in preventing the uprising that came to be known as Robert's Rebellion. When Lords Jon Arryn, Robert Baratheon, and Eddard Stark began their rebellion, Owen sent missives to the lords of the Seven Kingdoms declaring them outlaws and demanding their heads. He never stirred from King's Landing, and this coupled with the news of Ned and Robert's successful return to their respective seats of power made the paranoid Aerys believe that Lord Owen was conspiring with them. He was subsequently stripped of lands and titles and exiled for his failure, and was replaced as Hand of the King by Lord Jon Connington.[6]

King Robert I Baratheon eventually restored the Merryweather titles and some of their lands to Owen's grandson, Orton.[2]